ID code: '1RFR' CHIRALITY (03 Nov 1998) Checks the chirality and the naming of substituents of chiral and prochiral centers in nucleic acid structures. The molecular structure is read from a PDB file. Only the first model is evaluated. ---------------------------------------------------------- Center Reference for correct naming ---------------------------------------------------------- C1' alpha/beta nomenclature of anomeric sugars, base in beta position in natural nucleosids. C2' IUPAC. 1983. Eur J Biochem, 131: 9-15. C3' IUPAC. 1983. Eur J Biochem, 131: 9-15. C4' IUPAC. 1983. Eur J Biochem, 131: 9-15. C5' IUPAC. 1983. Eur J Biochem, 131: 9-15. P Brookhaven PDB entry '1BNA', O1P -> major groove, O2P -> minor groove. ---------------------------------------------------------- Author: Peter Slickers (slickers@imb-jena.de) Biocomputing, IMB Jena, Germany --------------------------------------------------------------------------------- Seq No Atom Residue H1' base O4' H1' base C2' --------------------------------------------------------------------------------- 9 C1' G A 1 alpha beta 4 27 10 7 43 C1' G A 2 alpha beta 38 61 44 41 77 C1' C A 3 alpha beta 72 92 78 75 108 C1' A A 4 alpha beta 103 125 109 106 141 C1' C A 5 alpha beta 136 156 142 139 172 C1' U A 6 alpha beta 167 187 173 170 202 C1' C A 7 alpha beta 197 217 203 200 233 C1' U A 8 alpha beta 228 248 234 231 263 C1' G A 9 alpha beta 258 281 264 261 297 C1' G A 10 alpha beta 292 315 298 295 331 C1' U A 11 alpha beta 326 346 332 329 361 C1' A A 12 alpha beta 356 378 362 359 394 C1' U A 13 alpha beta 389 409 395 392 424 C1' C A 14 alpha beta 419 439 425 422 455 C1' A A 15 alpha beta 450 472 456 453 488 C1' C A 16 alpha beta 483 503 489 486 519 C1' G A 17 alpha beta 514 537 520 517 553 C1' G A 18 alpha beta 548 571 554 551 587 C1' U A 19 alpha beta 582 602 588 585 617 C1' A A 20 alpha beta 612 634 618 615 650 C1' C A 21 alpha beta 645 665 651 648 681 C1' C A 22 alpha beta 676 696 682 679 712 C1' U A 23 alpha beta 707 727 713 710 742 C1' U A 24 alpha beta 737 757 743 740 772 C1' U A 25 alpha beta 767 787 773 770 802 C1' G A 26 alpha beta 797 820 803 800 836 C1' U A 27 alpha beta 831 851 837 834 866 C1' G A 28 alpha beta 861 884 867 864 900 C1' U A 29 alpha beta 895 915 901 898 930 C1' C A 30 alpha beta 925 946 931 928 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G A 1 OK OK 9 5 25 8 41 C2' G A 2 OK OK 43 39 59 42 75 C2' C A 3 OK OK 77 73 90 76 106 C2' A A 4 OK OK 108 104 123 107 139 C2' C A 5 OK OK 141 137 154 140 170 C2' U A 6 OK OK 172 168 185 171 200 C2' C A 7 OK OK 202 198 215 201 231 C2' U A 8 OK OK 233 229 246 232 261 C2' G A 9 OK OK 263 259 279 262 295 C2' G A 10 OK OK 297 293 313 296 329 C2' U A 11 OK OK 331 327 344 330 359 C2' A A 12 OK OK 361 357 376 360 392 C2' U A 13 OK OK 394 390 407 393 422 C2' C A 14 OK OK 424 420 437 423 453 C2' A A 15 OK OK 455 451 470 454 486 C2' C A 16 OK OK 488 484 501 487 517 C2' G A 17 OK OK 519 515 535 518 551 C2' G A 18 OK OK 553 549 569 552 585 C2' U A 19 OK OK 587 583 600 586 615 C2' A A 20 OK OK 617 613 632 616 648 C2' C A 21 OK OK 650 646 663 649 679 C2' C A 22 OK OK 681 677 694 680 710 C2' U A 23 OK OK 712 708 725 711 740 C2' U A 24 OK OK 742 738 755 741 770 C2' U A 25 OK OK 772 768 785 771 800 C2' G A 26 OK OK 802 798 818 801 834 C2' U A 27 OK OK 836 832 849 835 864 C2' G A 28 OK OK 866 862 882 865 898 C2' U A 29 OK OK 900 896 913 899 928 C2' C A 30 OK OK 930 926 944 929 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 39 C3' G A 2 OK OK 37 58 40 41 73 C3' C A 3 OK OK 71 89 74 75 104 C3' A A 4 OK OK 102 122 105 106 137 C3' C A 5 OK OK 135 153 138 139 168 C3' U A 6 OK OK 166 184 169 170 198 C3' C A 7 OK OK 196 214 199 200 229 C3' U A 8 OK OK 227 245 230 231 259 C3' G A 9 OK OK 257 278 260 261 293 C3' G A 10 OK OK 291 312 294 295 327 C3' U A 11 OK OK 325 343 328 329 357 C3' A A 12 OK OK 355 375 358 359 390 C3' U A 13 OK OK 388 406 391 392 420 C3' C A 14 OK OK 418 436 421 422 451 C3' A A 15 OK OK 449 469 452 453 484 C3' C A 16 OK OK 482 500 485 486 515 C3' G A 17 OK OK 513 534 516 517 549 C3' G A 18 OK OK 547 568 550 551 583 C3' U A 19 OK OK 581 599 584 585 613 C3' A A 20 OK OK 611 631 614 615 646 C3' C A 21 OK OK 644 662 647 648 677 C3' C A 22 OK OK 675 693 678 679 708 C3' U A 23 OK OK 706 724 709 710 738 C3' U A 24 OK OK 736 754 739 740 768 C3' U A 25 OK OK 766 784 769 770 798 C3' G A 26 OK OK 796 817 799 800 832 C3' U A 27 OK OK 830 848 833 834 862 C3' G A 28 OK OK 860 881 863 864 896 C3' U A 29 OK OK 894 912 897 898 926 C3' C A 30 OK OK 924 942 927 928 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 37 C4' G A 2 OK OK 39 57 36 38 71 C4' C A 3 OK OK 73 88 70 72 102 C4' A A 4 OK OK 104 121 101 103 135 C4' C A 5 OK OK 137 152 134 136 166 C4' U A 6 OK OK 168 183 165 167 196 C4' C A 7 OK OK 198 213 195 197 227 C4' U A 8 OK OK 229 244 226 228 257 C4' G A 9 OK OK 259 277 256 258 291 C4' G A 10 OK OK 293 311 290 292 325 C4' U A 11 OK OK 327 342 324 326 355 C4' A A 12 OK OK 357 374 354 356 388 C4' U A 13 OK OK 390 405 387 389 418 C4' C A 14 OK OK 420 435 417 419 449 C4' A A 15 OK OK 451 468 448 450 482 C4' C A 16 OK OK 484 499 481 483 513 C4' G A 17 OK OK 515 533 512 514 547 C4' G A 18 OK OK 549 567 546 548 581 C4' U A 19 OK OK 583 598 580 582 611 C4' A A 20 OK OK 613 630 610 612 644 C4' C A 21 OK OK 646 661 643 645 675 C4' C A 22 OK OK 677 692 674 676 706 C4' U A 23 OK OK 708 723 705 707 736 C4' U A 24 OK OK 738 753 735 737 766 C4' U A 25 OK OK 768 783 765 767 796 C4' G A 26 OK OK 798 816 795 797 830 C4' U A 27 OK OK 832 847 829 831 860 C4' G A 28 OK OK 862 880 859 861 894 C4' U A 29 OK OK 896 911 893 895 924 C4' C A 30 OK OK 926 941 923 925 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 OK OK 1 21 22 3 36 C5' G A 2 OK OK 35 55 56 37 70 C5' C A 3 OK OK 69 86 87 71 101 C5' A A 4 OK OK 100 119 120 102 134 C5' C A 5 OK OK 133 150 151 135 165 C5' U A 6 OK OK 164 181 182 166 195 C5' C A 7 OK OK 194 211 212 196 226 C5' U A 8 OK OK 225 242 243 227 256 C5' G A 9 OK OK 255 275 276 257 290 C5' G A 10 OK OK 289 309 310 291 324 C5' U A 11 OK OK 323 340 341 325 354 C5' A A 12 OK OK 353 372 373 355 387 C5' U A 13 OK OK 386 403 404 388 417 C5' C A 14 OK OK 416 433 434 418 448 C5' A A 15 OK OK 447 466 467 449 481 C5' C A 16 OK OK 480 497 498 482 512 C5' G A 17 OK OK 511 531 532 513 546 C5' G A 18 OK OK 545 565 566 547 580 C5' U A 19 OK OK 579 596 597 581 610 C5' A A 20 OK OK 609 628 629 611 643 C5' C A 21 OK OK 642 659 660 644 674 C5' C A 22 OK OK 673 690 691 675 705 C5' U A 23 OK OK 704 721 722 706 735 C5' U A 24 OK OK 734 751 752 736 765 C5' U A 25 OK OK 764 781 782 766 795 C5' G A 26 OK OK 794 814 815 796 829 C5' U A 27 OK OK 828 845 846 830 859 C5' G A 28 OK OK 858 878 879 860 893 C5' U A 29 OK OK 892 909 910 894 923 C5' C A 30 OK OK 922 939 940 924 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 32 P G A 2 distorted distorted 6 33 34 35 66 P C A 3 distorted distorted 40 67 68 69 97 P A A 4 distorted distorted 74 98 99 100 130 P C A 5 distorted distorted 105 131 132 133 161 P U A 6 distorted distorted 138 162 163 164 191 P C A 7 distorted distorted 169 192 193 194 222 P U A 8 distorted distorted 199 223 224 225 252 P G A 9 distorted distorted 230 253 254 255 286 P G A 10 distorted distorted 260 287 288 289 320 P U A 11 distorted distorted 294 321 322 323 350 P A A 12 distorted distorted 328 351 352 353 383 P U A 13 distorted distorted 358 384 385 386 413 P C A 14 distorted distorted 391 414 415 416 444 P A A 15 distorted distorted 421 445 446 447 477 P C A 16 distorted distorted 452 478 479 480 508 P G A 17 distorted distorted 485 509 510 511 542 P G A 18 distorted distorted 516 543 544 545 576 P U A 19 distorted distorted 550 577 578 579 606 P A A 20 distorted distorted 584 607 608 609 639 P C A 21 distorted distorted 614 640 641 642 670 P C A 22 distorted distorted 647 671 672 673 701 P U A 23 distorted distorted 678 702 703 704 731 P U A 24 distorted distorted 709 732 733 734 761 P U A 25 distorted distorted 739 762 763 764 791 P G A 26 distorted distorted 769 792 793 794 825 P U A 27 distorted distorted 799 826 827 828 855 P G A 28 distorted distorted 833 856 857 858 889 P U A 29 distorted distorted 863 890 891 892 919 P C A 30 distorted distorted 897 920 921 922 ---------------------------------------------------------------------------------